AMAP

AMAP is a multiple alignment tool that aims to maximize the expected Alignment Metric Accuracy by "annealing" pairs of homologous residues.

• http://baboon.math.berkeley.edu/amap/
• AMAP (Wikipedia)
• Schwartz AS, Pachter L.  Multiple alignment by sequence annealing.  Bioinformatics. 2007 Jan 15;23(2):e24-9.
• Casa Software